Hi John,

this error looks familiar:
https://github.com/galaxyproject/galaxy/issues/3178
https://github.com/galaxyproject/galaxy/issues/4153
https://github.com/galaxyproject/starforge/issues/130

To remedy the 'option' error:

source /home/galaxy/galaxy/.venv/bin/activate
pip install --upgrade python-ldap


Hope this brings you a step further.

- Jelle

On Wed, Jun 14, 2017 at 6:09 PM, John Chen <jchen...@yahoo.com> wrote:

> Jelle
>
> I did all that and it looks correct.. it is retrieving the correct field.
> This is the error i am still getting..  I am using pretty much the same
> option in other apps..
>
>
>
> galaxy.webapps.galaxy.controllers.user DEBUG 2017-06-14 12:04:40,648
> trans.app.config.auth_config_file: ./config/auth_conf.xml
> galaxy.auth.providers.ldap_ad DEBUG 2017-06-14 12:04:40,648 LDAP
> authenticate: email is johnu...@example.org
> galaxy.auth.providers.ldap_ad DEBUG 2017-06-14 12:04:40,648 LDAP
> authenticate: username is None
> galaxy.auth.providers.ldap_ad DEBUG 2017-06-14 12:04:40,648 LDAP
> authenticate: options are {'bind-user': '{dn}', 'search-fields':
> 'uid,mail', 'login-use-username': 'False', 'allow-register': 'True',
> 'ldap-options': 'OPT_X_TLS_REQUIRE_CERT=OPT_X_TLS_ALLOW',
> 'auto-register-email': '{email}', 'server': 'ldap://ldap.nyumc.org',
> 'auto-register': 'True', 'search-base': 'DC=example,DC=org',
> 'search-filter': '(mail={email})', 'continue-on-failure': 'True',
> 'auto-register-username': '{sAMAccountName', 'bind-password': '{password}',
> 'allow-password-change': 'False'}
> galaxy.auth.providers.ldap_ad DEBUG 2017-06-14 12:04:40,648 LDAP
> authenticate: Valid LDAP option pair OPT_X_TLS_REQUIRE_CERT=OPT_X_TLS_ALLOW
> -> 24582=3
> galaxy.auth.providers.ldap_ad ERROR 2017-06-14 12:04:40,648 LDAP
> authenticate: search exception
> Traceback (most recent call last):
>   File "/home/galaxy/galaxy/lib/galaxy/auth/providers/ldap_ad.py", line
> 118, in authenticate
>     ldap.set_option(*opt)
>   File 
> "/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/ldap/functions.py",
> line 135, in set_option
>     return _ldap_function_call(None,_ldap.set_option,option,invalue)
>   File 
> "/home/galaxy/galaxy/.venv/lib/python2.7/site-packages/ldap/functions.py",
> line 66, in _ldap_function_call
>     result = func(*args,**kwargs)
> ValueError: option error
>
>
> Are you running MS AD ?   if so, could i take a look at your config file?
>
> Thanks
> John
>
>
> ------------------------------
> *From:* Jelle Scholtalbers <j.scholtalb...@gmail.com>
> *To:* Hans-Rudolf Hotz <h...@fmi.ch>
> *Cc:* John Chen <jchen...@yahoo.com>; Galaxy Dev List <galaxy-dev@lists.
> galaxyproject.org>
> *Sent:* Monday, June 12, 2017 3:16 AM
> *Subject:* Re: [galaxy-dev] AD Intergration
>
> Hi John,
>
> as a tip, you can use the tool "ldapsearch", from e.g. the package
> "openldap-client", to figure out with which attributes you search and which
> attributes you can retrieve.
>
> Examples:
> $ ldapsearch -vv -x -H ldap://dc1.example.com -b
> cn=Users,dc=exampke,dc=org" # retrieve all AD/ldap entries
> $ ldapsearch -vv -x -H ldap://dc1.example.com -b
> cn=Users,dc=exampke,dc=org "uid=a_username"  # retrieve all attributes for
> user with uid "a_username"
> $ ldapsearch -vv -x -H ldap://dc1.example.com -b
> cn=Users,dc=exampke,dc=org "sAMAccountName=a_username" mail # only
> retrieve the mail attribute by searching for the sAMAccountName
>
>
> In addition, if you get it working, you might want to switch to the more
> secure ldap*s* if that is supported by your IT.
>
> Cheers,
> Jelle
>
>
>
> On Mon, Jun 12, 2017 at 8:32 AM, Hans-Rudolf Hotz <h...@fmi.ch> wrote:
>
>
>
> On 06/09/2017 03:29 PM, John Chen wrote:
>
> Hans-Rudolf,
>
> That got me past the error, but I i am now having issue authenticating
> with against AD, as if its not able to search for the users.  Do I need
> a binding service account to search AD object?  Does the bottow 5 lines
> look correct?
>
>
> They look right, but I can't say whether they are correct. You need to
> discuss this with the person who has set up your Active Directory
>
>
> Hans-Rudolf
>
>
>
>
> <search-base>cn=galaxy,ou=Secu rity,ou=somegroup,dc=example,
> dc=org</search-base>
>
> <search-filter>(&amp;(objectCl ass=user)(sAMAccountName={
> username}))</search-filter>
>              <search-user>ADsearchAccount< /search-user>
>              <search-password>AD_Search_Pa sswrd</search-password>
>              <bind-user>{sAMAccountName}</ bind-user>
>
> The logs show that it found the userID and email, but gets an invalid
> password on the webportal
>
> galaxy.webapps.galaxy.controll ers.user DEBUG 2017-06-09 09:26:34,592
> trans.app.config.auth_config_f ile: ./config/auth_conf.xml
> galaxy.auth.providers.ldap_ad DEBUG 2017-06-09 09:26:34,592 LDAP
> authenticate: email is testuser.n...@example.org
> galaxy.auth.providers.ldap_ad DEBUG 2017-06-09 09:26:34,592 LDAP
> authenticate: username is testUser
> galaxy.auth.providers.ldap_ad DEBUG 2017-06-09 09:26:34,592 LDAP
> authenticate: options are {'bind-user': '{sAMAccountName}',
> 'search-fields': 'sAMAccountName,mail', 'login-use-username': 'True',
> 'allow-register': 'False', 'auto-register-email': '{mail}', 'server':
> 'ldap://xxx.xxx.xx', 'auto-register': 'True', 'search-base':
> 'cn=xxx-xx,ou=Security,ou=xxxx x xxx,dc=xxx,dc=xx', 'search-filter':
> '(&(objectClass=user)(sAMAccou ntName={username}))',
> 'auto-register-username': '{sAMAccountName}', 'search-password': 'xxxx',
> 'search-user': 'xxxx', 'bind-password': '{password}'}
> galaxy.auth.providers.ldap_ad WARNING 2017-06-09 09:26:34,596 LDAP
> authenticate: search returned no results
> 10.127.220.227 - - [09/Jun/2017:09:26:34 -0400] "POST
> /user/login?use_panels=False HTTP/1.1" 200 -
> "http://glxlcdcpvm01.nyumc.org :8080/user/login?use_panels= False
> <http://glxlcdcpvm01.nyumc.org:8080/user/login?use_panels=False>"
> "Mozilla/5.0 (Windows NT 10.0; WOW64; rv:53.0) Gecko/20100101 Firefox/53.0"
>
>
> ------------------------------ ------------------------------ ------------
> *From:* Hans-Rudolf Hotz <h...@fmi.ch>
> *To:* John Chen <jchen...@yahoo.com>; Galaxy Dev List
> <galaxy-dev@lists.galaxyprojec t.org <galaxy-dev@lists.galaxyproject.org>>
> *Sent:* Friday, June 9, 2017 3:34 AM
> *Subject:* Re: [galaxy-dev] AD Intergration
>
> always keep the mailing list in the loop! in order for others to help or
> learn
>
>
>
> On 06/08/2017 07:27 PM, John Chen wrote:
>  > Hans-Rudolf
>  >
>  > This is the error I get when I start the Galaxy server.
>  >
> ...
>  > xml.etree.ElementTree.ParseErr or: mismatched tag: line 8, column 105
>  >
>
> This is very informative. Looking at line 8 in your file:
>
>
> <server><a class="moz-txt-link-freetext"
> href="ldap://ldap.xxx.xx";>ldap ://ldap.xxx.xx</server>
>
>
> The element "a" is not  terminated
>
>
> What happens, if you try just
>
> <server>ldap://ldap.xxx.xx</se rver>
>
>
>
>
>
> Regards, Hans-Rudolf
>
>
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>
>
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